NHGRI Seeks Next Generation of Sequencing Technologies

New Grants Support Development of Faster, Cheaper DNA Sequencing

BETHESDA, Md., Thurs., Oct. 14, 2004 - The National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), today announced it has awarded more than $38 million in grants to spur the development of innovative technologies designed to dramatically reduce the cost of DNA sequencing, a move aimed at broadening the applications of genomic information in medical research and health care.

NHGRI's near-term goal is to lower the cost of sequencing a mammalian-sized
genome to $100,000, which would enable researchers to sequence the genomes of
hundreds or even thousands of people as part of studies to identify genes that
contribute to cancer, diabetes and other common diseases. Ultimately, NHGRI's
vision is to cut the cost of whole-genome sequencing to $1,000 or less, which
would enable the sequencing of individual genomes as part of medical care. The
ability to sequence each person's genome cost-effectively could give rise to
more individualized strategies for diagnosing, treating and preventing disease.
Such information could enable doctors to tailor therapies to each person's unique
genetic profile.

DNA sequencing costs have fallen more than 100-fold over the past decade, fueled
in large part by tools, technologies and process improvements developed as part
of the successful effort to sequence the human genome. However, it still costs
at least $10 million to sequence 3 billion base pairs - the amount of DNA found
in the genomes of humans and other mammals.

"These grants will open the door to the next generation of sequencing
technologies. There are still many opportunities to reduce the cost and increase
the throughput of DNA sequencing, as well as to develop smaller, faster sequencing
technologies that meet a wider range of needs," said NHGRI Director Francis
S. Collins, M.D., Ph.D. "Dramatic reductions in sequencing costs will lead
to very different approaches to biomedical research and, eventually, will revolutionize
the practice of medicine."

In the first set of grants, 11 teams will work to develop "near term"
technologies that, within five years, are expected to provide the power to sequence
a mammalian-sized genome for about $100,000. In the second set, seven groups
will take on the longer-term challenge of developing revolutionary technologies
to realize the vision of sequencing a human genome for $1,000 or less. The approaches
pursued by both sets of grants have many complementary elements that integrate biochemistry,
chemistry and physics with engineering to enhance the whole effort to develop
the next generation of DNA sequencing and analysis technologies.

"These projects span an impressive spectrum of novel technologies - from
sequencing by synthesis to nanopore technology. Many of these new approaches
have shown significant promise, yet far more exploration and development are
needed if these sequencing technologies are to be useful to the average researcher
or physician," said Jeffery Schloss, Ph.D., NHGRI's program director for
technology development. "We look forward to seeing which of these technologies
fulfill their promise and achieve the quantum leaps that are needed to take
DNA sequencing to the next level."

"$100,000" Genome Grants

NHGRI's "Near-Term Development for Genome Sequencing" grants will
support research aimed at sequencing a human-sized genome at 100 times lower
cost than is possible today. There is strong potential that, five years from
now, some of these technologies will be at or near commercial availability.
Grant recipients and their approximate total funding are:

Stevan B. Jovanovich, Ph.D., Microchip Biotechnologies Inc., Fremont, Calif.
$6.1 million (3 years)
"Microbead INtegrated DNA Sequencer (MINDS) System"
Retaining the advantages of current DNA sequencing methods, including well-developed
community infrastructure, commercial availability of reagents and existing analysis
software, this group will push Sanger-based sequencing toward its performance
limit in a completely automated, bench-top system. The heart of the system will
be a microchip-based device that can label and process DNA fragments from individual
microbeads in low-volume reactions, followed by ultra-fast separation and analysis
on microfabricated capillary electrophoresis channels.

Gina L. Costa, Ph.D., Agencourt Bioscience Corp., Beverly, Mass.
$5.4 million (3 years)
"Bead-based Polony Sequencing"
This group will work to further develop polymerase colony (polony) sequencing
technologies. This is a highly parallel sequencing approach that involves synthesizing
short regions of identical DNA fragments on magnetic beads, packing millions
of them into a chamber and then extending each of those molecules while detecting
the addition of fluorescently labeled DNA building blocks or nucleotides.

Kenton Lohman, Ph.D., 454 Life Sciences Corp., Branford, Conn.
$2 million (2 years)
"Massively Parallel High Throughput, Low Cost Sequencing"
and
Marcel Margulies, Ph.D., 454 Life Sciences Corp., Branford, Conn.
$5 million (3 years)
"454 Life Sciences Massively Parallel System DNA Sequencing"
Expanding the capabilities of its sequencing-by-synthesis technology, this group
will scale up the system to increase throughput, cut costs and provide the power
to sequence genomes of organisms for which no framework of genomic data exists.
In order to reduce labor and costs, this method emphasizes the miniaturization
of each step, from sample preparation to DNA sequencing. The platform enables
one person to fragment, amplify, sequence and assemble an entire genome, regardless
of the genome's size.

John Williams, Ph.D., LI-COR Inc., Lincoln, Neb.
$2.5 million (3 years)
"Single-Molecule DNA Sequencing Using Charge-Switch dNTPs"
Sequencing single molecules produces challenges in imaging, but reduces other
hurdles to achieving long sequence read length. This group is developing technology
to detect the release of reaction products when nucleotides are incorporated
into single DNA strands.

Michael L. Metzker, Ph.D., Human Genome Sequencing Center, Baylor College of
Medicine, Houston
$2 million (3 years)
"Ultrafast SBS (Sequencing by Synthesis) Method for Large-Scale Human Resequencing"
This team will focus on developing novel fluorescent, photolabile nucleotide
terminators for sequencing by synthesis, as well as making improvements to enzymes
called DNA polymerases that will support their accurate incorporation into DNA.
This is part of the group's plan to eventually build a full-scale sequencing
system.

Stephen R. Quake, Ph.D., Stanford University, Palo Alto, Calif.
$1.8 million (3 years)
"High-Throughput, Single-Molecule DNA Sequencing"
This group will try to improve its sequencing-by-synthesis technology in order
to achieve longer reads from very large numbers of single DNA molecules. The
key to the technology's single molecule sensitivity is the detection of fluorescence
resonance energy transfer on a total internal reflection microscope.

Mostafa Ronaghi, Ph.D., Stanford Genome Technology Center, Palo Alto, Calif.
$1.8 million (3 years)
"Pyrosequencing Array for DNA Sequencing"
The principal investigator of this team is an inventor of pyrosequencing, which
uses unmodified nucleotides and polymerases to synthesize DNA and a firefly
enzyme to generate a chemiluminescent signal. The group of researchers will
work on further developing a highly integrated and parallel format with improved
equipment for detection of the chemiluminescent signals resulting in a portable
and inexpensive device for low-cost genome sequencing.

Jingyue Ju, Ph.D., Columbia University, New York
$1.8 million (3 years)
"An Integrated System for DNA Sequencing by Synthesis"
One focus of this team's research is novel chemistry that allows a fluorescent
molecule attached to a nucleotide to be detected and then removed with a flash
of light after its addition to a growing DNA molecule. The researchers will
also develop a unique way to attach many thousands of DNA molecules site specifically
to a surface to produce a high-throughput device for DNA sequencing by synthesis.

Peter Williams, Ph.D., Arizona State University, Tempe
$1.7 million (3 years)
"Multiplexed Reactive Sequencing of DNA"
This group will use commercially available, fluorescein-labeled nucleotides
and off-the-shelf detectors in a practical sequencing-by-synthesis system multiplexed
to read more than 10,000 sequences simultaneously. The system will be targeted
initially at specific genes and subsequently at whole genomes.

Steven A. Benner, Ph.D., University of Florida, Gainesville
$800,000 (3 years)
"Polymerases for Sequencing by Synthesis"
This group's goal is to engineer a DNA polymerase, which is the enzyme used
in cells and in laboratory experiments to synthesize new DNA molecules, that
will have optimal characteristics for sequencing by synthesis with chemically-altered
nucleotides.

Amit Meller, Ph.D., Rowland Institute at Harvard, Harvard University, Cambridge, Mass.
$600,000 (2 years)
"Ultra-fast Nanopore Readout Platform for Designed DNA's"
A nanometer is one-billionth of a meter, much too small to be seen with a conventional
lab microscope. Most groups developing nanopores (holes about 2 nm in diameter)
as DNA sequence transducers propose to detect an electrical, or ionic, signal
from individual DNA molecules. This group will pursue a novel approach in which
a nanopore is used to simultaneously detect electrical and fluorescent signals
from many nanopores at one time.

"$1,000 Genome" Grants

NHGRI's "Revolutionary Genome Sequencing Technologies" grants have
as their goal the development of breakthrough technologies that will enable
a human-sized genome to be sequenced for $1,000 or less. Grant recipients and
their approximate total funding are:

J. Michael Ramsey, Ph.D., University of North Carolina, Chapel Hill
$2 million (2 years)
Nanotechnology for the Structural Interrogation of DNA
This group will explore combinations of fabrication technologies to build devices
for analysis of single DNA molecules, and use various measurement techniques
to extract information from those devices. Experiment is woven together with
simulation and modeling to understand the basic physics of molecule-device interaction
at this size scale and its implications for device design.

James Weifu Lee, Ph.D., Oak Ridge National Laboratory, Oak Ridge, Tenn.
Two grants: $700,000 (3 years); $750,000 (3 years)
"Computational Research & Development for Rapid Sequencing Nanotechnology"
"Experimental Research & Development for Rapid Sequencing Nanotechnology"
This group will develop computational modeling to guide the fabrication of a
novel nanotechnology sequencing device, as well as design electronic control
and detection experiments. Using this information, the group will build a device
in which stretched DNA molecules would be made to pass between sharp electrodes
spaced 2 to 5 nanometers apart. It will then test the device to see if it is
possible to distinguish between the four types of nucleotides based on differences
in a phenomenon called electron tunneling.

Scott D. Collins, Ph.D., University of Maine, Orono
$850,000 (2 years)
"High-speed Nanopore Gene Sequencing"
Skilled in silicon fabrication methods, this group will try to fabricate a nanopore
with tiny electrodes and built-in circuits that will be used in experiments
that attempt to measure differences in the electron tunneling of individual
nucleotides in DNA molecules. Such devices could lay the groundwork for high-speed
approaches to sequencing single DNA molecules.

Steven A. Benner, Ph.D., University of Florida, Gainesville
$800,000 (3 years)
"DNA Sequencing Using Nanopores"
This group will produce conical nanopores in a synthetic membrane, coat the
pores with gold, modify the pores to control DNA transport and then introduce
chemically modified DNA. The goal will be to detect different signals from each
of the four types of nucleotides as DNA passes through the pores.

Andre Marziali, Ph.D., University of British Columbia, Vancouver
$650,000 (3 years)
"Nanopores for Trans-Membrane Bio-Molecule Detection"
This group will contribute to understanding how single biological molecules
interact with pores inserted into membranes, and how useful information can
be derived from those interactions. This study attempts to extend the use of
nanopore sensors into living cells.

Stuart Lindsay, Ph.D., Arizona State University, Tempe, Ariz.
$550,000 (3 years)
"Molecular Reading Head for Single-Molecule DNA Sequencing"
Building on the concept of threading DNA through a molecular pore, this group
is developing a system in which a chemical ring, acting as a reading head, is
used to measure differences in friction as DNA passes through the ring. Theory
and experiment are used to understand the observations.

Ronald W. Davis, Ph.D., Stanford University, Stanford, Calif.
$450,000 (2 years)
"Single Molecule Nucleic Acid Detection with Nanopipettes"
This group takes a stepwise approach to single nucleic acid molecule detection,
using the nanoscale pore in a pulled glass pipette to measure single DNA molecules
with attached nanoparticles. Understanding the electrical signals produced by,
and the limits of this technology will contribute to next-generation devices
with higher informational content.

"Each of these projects brings a unique combination of approach and expertise
to solving difficult scientific and engineering problems. Collectively, this
balanced grant portfolio should galvanize the sequencing technology research
community and accelerate the substantial leaps forward needed to achieve substantial
reduction in DNA sequencing costs," said Mark S. Guyer, Ph.D., director
of NHGRI's Division of Extramural Research, which supports grants for research
and for training and career development at sites nationwide.